Potential relationships between amino acid motifs in the antigen binding groove of various alleles of the bovine major histocompatibility complex DR (BoLA-DR) molecule and occurrence of clinical mastitis caused by Staphylococcus species (non-Staphylococcus aureus) were investigated in a case-control study. A significant association (P< or =0.05) was detected between the presence of glutamic acid at position beta 74 and occurrence of mastitis caused by Staphylococcus spp. with a relative risk of 11. This motif is present in BoLA-DRB3.2*22, *23 and *24 alleles. Presence of a positively charged residue (arginine or lysine) at position 13 also showed a tendency (P< o r=0.1) towards an association with a higher risk of clinical mastitis caused by the same bacteria. This motif is present in BoLA-DRB3.2*23 and *8 alleles. Similarly, presence of arginine at position beta 71 (present in alleles *23 and *22) was associated with occurrence of this disease. These positions (beta 13, beta 71 and beta 74) form pocket 4 of the antigen binding groove, which plays an instrumental role in antigen binding and recognition by T-lymphocytes. Thus, it can be concluded that pocket 4 of the BoLA-DR molecule is involved in conferring susceptibility to clinical mastitis caused by Staphylococcus spp.